File Download

There are no files associated with this item.

  Links for fulltext
     (May Require Subscription)
Supplementary

Article: AC-DIAMOND v1: Accelerating large-scale DNA-protein alignment.

TitleAC-DIAMOND v1: Accelerating large-scale DNA-protein alignment.
Authors
Issue Date2018
Citation
Bioinformatics, 2018 How to Cite?
AbstractSUMMARY: AC-DIAMOND (v1) is a DNA-protein alignment tool designed to tackle the efficiency challenge of aligning large amount of reads or contigs to protein databases. When compared with the previously most efficient method DIAMOND, AC-DIAMOND gains a 6- to 7-fold speed-up, while retaining a similar degree of sensitivity. The improvement is rooted at two aspects: first, using a compressed index of seeds with adaptive-length to speed up the matching between query and reference sequences; second, adopting a compact form of dynamic programming to fully utilize the parallelism of the SIMD capability. AVAILABILITY: Software source codes and binaries available at https://github.com/Maihj/AC-DIAMOND/. CONTACT: hjmai@cs.hku.hk, hfting@cs.hku.hk, twlam@cs.hku.hk. SUPPLEMENTARY INFORMATION: Benchmark data & results https://sourceforge.net/projects/ac-diamond-v1/files/data/.
Persistent Identifierhttp://hdl.handle.net/10722/259908
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorMAI, H-
dc.contributor.authorZHANG, Y-
dc.contributor.authorLI, D-
dc.contributor.authorLeung, HCM-
dc.contributor.authorLuo, R-
dc.contributor.authorWong, C-
dc.contributor.authorTing, HF-
dc.contributor.authorLam, TW-
dc.date.accessioned2018-09-03T04:16:18Z-
dc.date.available2018-09-03T04:16:18Z-
dc.date.issued2018-
dc.identifier.citationBioinformatics, 2018-
dc.identifier.urihttp://hdl.handle.net/10722/259908-
dc.description.abstractSUMMARY: AC-DIAMOND (v1) is a DNA-protein alignment tool designed to tackle the efficiency challenge of aligning large amount of reads or contigs to protein databases. When compared with the previously most efficient method DIAMOND, AC-DIAMOND gains a 6- to 7-fold speed-up, while retaining a similar degree of sensitivity. The improvement is rooted at two aspects: first, using a compressed index of seeds with adaptive-length to speed up the matching between query and reference sequences; second, adopting a compact form of dynamic programming to fully utilize the parallelism of the SIMD capability. AVAILABILITY: Software source codes and binaries available at https://github.com/Maihj/AC-DIAMOND/. CONTACT: hjmai@cs.hku.hk, hfting@cs.hku.hk, twlam@cs.hku.hk. SUPPLEMENTARY INFORMATION: Benchmark data & results https://sourceforge.net/projects/ac-diamond-v1/files/data/.-
dc.languageeng-
dc.relation.ispartofBioinformatics-
dc.titleAC-DIAMOND v1: Accelerating large-scale DNA-protein alignment.-
dc.typeArticle-
dc.identifier.emailLeung, HCM: cmleung3@hku.hk-
dc.identifier.emailLuo, R: rbluo@cs.hku.hk-
dc.identifier.emailTing, HF: hfting@cs.hku.hk-
dc.identifier.emailLam, TW: twlam@cs.hku.hk-
dc.identifier.authorityLeung, HCM=rp00144-
dc.identifier.authorityLuo, R=rp02360-
dc.identifier.authorityTing, HF=rp00177-
dc.identifier.authorityLam, TW=rp00135-
dc.identifier.doi10.1093/bioinformatics/bty391-
dc.identifier.hkuros289196-
dc.identifier.isiWOS:000450038900020-

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats